Early detection of breast cancer improves the chances of successful treatment and recovery. Routine screening mammography has increased the detection of stage I breast cancers and correspondingly, many more women are being diagnosed with lymph node-negative tumors (B. Cady, 1997, Surg Oncol Clin N Am 6:195-202). About 43% of the approximately 240,000 women in the United States diagnosed with breast cancer each year are node-negative (no detectable tumor cells in lymph nodes).
Based on the current guidelines, 85-90% of node-negative patients are candidates for systemic adjuvant therapy after surgery. Such systemic adjuvant therapy may include chemotherapy and hormonal therapy. However, about 60-70% of women with node-negative breast cancer who receive local treatment (mastectomy or lumpectomy and radiation) will not experience distant recurrence. Treatment decisions for breast cancer patients benefit from the assessment of each patient's risk for metastasis and response to treatment using multiple clinical and histopathological parameters.
Several recent studies have used microarrays to demonstrate that a patient's gene expression profile can also provide useful prognostic information. A subset of these studies has received focused attention due to their size, and the extent of their validation. (L J van't Veer, H. Dai et al., 2002, Nature 415:530-536; M J van de Vijver, Y D He et al., 2002, N Engl J Med 347:1999-2009; Y. Wang, J G Klijn et al., 2005, Lancet 365:671-679; H. Dai, L J van't Veer et al., 2005, Cancer Res 15:4059-4066; and H Y Chang, D S Nuyten et al., 2005, Proc Natl Acad Sci USA 102:3738-3743).
The resulting confidence garnered for a 70-gene prognostic signature identified by van't Veer, Dai et al. (2002, Nature 415:530-536) has led to its incorporation into a European trial, the Microarray for Node-Negative Disease May Avoid Chemotherapy (MINDACT). Likewise, a PCR-based, 21-gene predictive signature described by S P Paik, S. Shak et al. (2004, N Engl J Med 351:2817-2826) has been included in a phase III trial by The Breast Cancer Intergroup of North America (Program for the Assessment of Clinical Cancer Tests (PACCT) (V G Kaklamani and W J Gradishar, 2006, Curr Treat Options Oncol 7:123-8).
The 21-gene predictive signature (including 5 normalization genes) by S P Paik (2004, N Engl J Med 351:2817-2826) was derived from Tamoxifen-treated patients. The independence of that signature has drawn concern due to its substantial overlap with genes and/or proteins already used in conventional immunohistochemistry (IHC) tests (D R Carrizosa and L A Carey, 2005, The American Journal of Oncology Review 4:7-10). Various hormonal therapy strategies for treating ER-positive breast cancer patients may include Tamoxifen alone, sequential use of Tamoxifen plus aromatase inhibitors, or aromatase inhibitors alone (E P Winer, C. Hudis et al., 2005, J Clin Oncol 23: 619-629; S M Swain, 2005, N Engl J Med 353:2807-9).
Thus, there is a need for a gene-based prognostic assay that can be used for routine clinical laboratory testing in predicting the risk of distant metastasis in breast cancer patients, particularly an assay that detects expression levels mRNA, which can be readily obtained from tumor tissues preserved by routine collection methods such as FFPE tumor sections. Information about the risk for distant metastasis can be used in guiding treatment strategies for breast cancer patients, particularly early stage lymph node-negative patients, such that patients who are at higher risk of distant metastasis are treated properly, and patients who are at lower risk of distant metastasis may be spared the side effects of certain treatments.
A 14-gene metastasis score, which is particularly useful for determining risk of distant metastasis in a breast cancer patient, is described in U.S. Pat. No. 7,695,915, issued Apr. 13, 2010 to Kit Lau et al., which is incorporated herein by reference in its entirety.
Progesterone Receptor (PR)
Progesterone receptor (PR) status, as well as estrogen receptor (ER) status, in breast cancer patients is a factor that is used for therapeutic decisions such as whether or not a patient may benefit from hormonal therapy (Henry and Hayes, Oncologist 2006, 11:541-552) (PGR is the gene name for PR, thus PR and PGR may be used herein interchangeably; ESR1 is the gene name for ER, thus ER and ESR1 may be used herein interchangeably). The American Society of Clinical Oncology (ASCO) recommends routine measurement of PR, as well as ER, to identify patients most likely to benefit from hormonal therapy (Harris et al., J Clin Oncol 2007, 25:5287-5312). As an example, studies have shown that patients with ER-positive/PR-negative breast tumors responded less well to hormonal therapy than those with ER-positive/PR-positive breast tumors (Kim et al., Clin Cancer Res 2006, 12: 1013s-1018s and Cui et al., J. Clin Oncol 2005; 23: 7721-7735). In Caucasians, approximately 60-65% of breast cancer cases are ER-positive and PR-positive (ER+/PR+), 15-20% are ER+/PR−, 15-20% are ER−/PR−, and less than 5% are ER−/PR+ (Anderson et al., J Clin Oncol 2001, 19:18-27). The estrogen receptor is the therapeutic target for tamoxifen, a selective estrogen receptor modulator (SERM) that is commonly used in the treatment of breast cancer. ER and PR status in malignant tissue from breast cancer patients provides classification of outcome and clinical benefit for adjuvant endocrine or chemoendocrine therapies such as tamoxifen and aromatase inhibitors. The response rate to tamoxifen treatment has been reported to be markedly decreased in patients with ER+/PR− breast tumors (Cui et al., J Clin Oncol 2005, 23:7721-7735; Arpino et al., J Natl Cancer Inst 2005, 97:1254-1261; and Rakha et al., J Clin Oncol 2007, 25:4772-4778).
In accordance with conventional terminology, PR (as well as ER) “status” refers to the relative expression level of this gene in a breast tumor sample as compared with the normal range of expression levels of this gene in healthy (i.e., non-cancerous) breast samples. The term “positive” with respect to PR (as well as ER) status indicates that the gene is over-expressed in a breast tumor. In contrast, “negative” indicates that the gene is not over-expressed in a breast tumor.
The status of PR (as well as ER) can be evaluated using immunohistochemistry (IHC). One example of IHC testing is a semi-quantitative IHC interpretation system, the Allred score, which was developed to grade immunostained slides based upon the percentage and intensity of positively stained tumor cells.
The status of PR (as well as ER) can be evaluated using nucleic acid-based assays. For example, molecular assays such as gel-based, semi-quantitative RT-PCR assays (Chevillard et al., Breast Cancer Res Treat 1996, 41:81-89; Tong et al., Anal Biochem 1997, 251:173-177; Hackl et al., Anticancer Res 1998, 18:839-842; Shepard et al., Mod Pathol. 2000, 13:401-406; and Tong et al., Clin Cancer Res 1999, 5:1497-1502) and quantitative assays using real-time RT-PCR and nucleic acid sequence-based amplification (NASBA) technologies (Iwao et al., Cancer 2000, 89:1732-1738; de Cremoux et al., Endocr Relat Cancer 2004, 11:489-495; Labuhn et al., Int J Biol Markers 2006, 21:30-39; and Lamy et al., Clin Chem Lab Med 2006: 44:3-12) have been developed to measure the mRNA level of PR in frozen breast biopsy tissue samples. TaqMan® RT-PCR assays to quantitate PR mRNA levels in archived formalin-fixed, paraffin-embedded (FFPE) specimens have been reported (Cronin et al., Am J Pathol 2004, 164:35-42 and Ma et al., J Clin Oncol 2006, 24:4611-4619). Lamy et. al. (Clin Chem Lab Med 2006: 44:3-12) developed a duplex real-time NASBA assay using molecular beacon probes to measure mRNA levels of PGR along with the housekeeping gene PPIB. The results were then compared to a duplex quantitation curve to determine the hormonal receptor mRNA level in frozen tissue samples. Labuhn et. al. (Int J Biol Markers. 2006, 21:30-39) developed simplex TaqMan® assays to determine mRNA levels of PGR along with housekeeping gene 18S.
Nucleic acid-based assays of PR are also described in U.S. patent application Ser. No. 12/355,873, filed Jan. 19, 2009 by Sheng-Yung Chang et al., which is incorporated herein by reference in its entirety, particularly those portions of Ser. No. 12/355,873 which relate to PR.